Efficient implementations of Needleman-Wunsch and other sequence alignment algorithms written in Rust with Python bindings via PyO3.

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SneakySnake:snake: is the first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU architectures. It greatly (by more than two orders of magnitude) expedites sequence alignment calculation for both short and long reads. Described in the Bioinformatics (2020) by Alser et al. https://arxiv.o…

Needleman-Wunsch and Smith-Waterman algorithms in python

Interactive Visualization of Needleman-Wunsch Algorithm in Javascript

Collection of sequence alignment algorithms.

Generate an accurate, timestamped transcript given an audio file and its text using Google Cloud's Speech-to-Text API via gRPC.

Implementation of Needleman-Wunsch algorithm in Python Using Nested Functions.

Tool for exploring sequence alignment algorithms

Implementation of Needleman-Wunsch, Smith-Waterman, Hirschberg and affine bioinformatics algorithms for alighning biological sequences

A Python module to calculate alignment between two sequences using EMBOSS' needle, stretcher, and water

Short implementation (~500 lines) of the Gotoh algorithm, a.k.a. Needleman-Wunsch with affine gap penalties.

This is the implementation of 3rd Part in 3-Part Series of Algorithms Illuminated Book. All Implementations in this repository are written in both Python and Golang. Single IPython Notebook contains all Algorithms given in this Part 3.

Cython bindings and Python interface to Opal, a SIMD-accelerated database search aligner.

Less-wrong single-file Numba-accelerated Python implementation of Gotoh affine gap penalty extensions for the Needleman–Wunsch, Smith-Waterman, and Levenshtein algorithms for sequence alignment

The first work to provide a comprehensive survey of a prominent set of algorithmic improvement and hardware acceleration efforts for the entire genome analysis pipeline used for the three most prominent sequencing data, short reads (Illumina), ultra-long reads (ONT), and accurate long reads (HiFi). Described in arXiv (2022) by Alser et al. https…

🔬 🏁 Comparison of DNA Sequences

A systematic survey of algorithmic foundations and methodologies across 107 alignment methods (1988-2021), for both short and long reads. We provide a rigorous experimental evaluation of 11 read aligners to demonstrate the effect of these underlying algorithms on speed and efficiency of read alignment. Described by Alser et al. at https://arxiv.…

Use the Needleman-Wunsch algorithm to align two sequences: s1 and s2. Assume that a match = +2, mismatch = -2, gap = -2

Sequence alignment algorithms